screening for dinucleotide/trinucleotide repeats in sequence

Anders Gorm Pedersen gorm at cbs.dtu.dk
Wed May 24 04:27:48 EST 2000


"Gorry, Mike" wrote:
> 
> Is anyone aware of a program/algorithm available that will screen large
> segments of sequenced DNA (BACs or PACs) for dinucleotide/trinucleotide 
> repeats that have not already been identified? 
> 
> Thanks
> 
> Michael Gorry
> gorrym at cpc.pitt.edu

I think the tandem repeats finder is what you need:

http://c3.biomath.mssm.edu/trf.html 

There's a web-server and you can download your own copy of the program.

Hoep this helps,
Anders Gorm Pedersen.

Here's the reference:

G. Benson,
"Tandem repeats finder: a program to analyze DNA sequences"
Nucleic Acids Research (1999)
Vol. 27, No. 2, pp. 573-580.


A tandem repeat in DNA is two or more adjacent, approximate copies of a
pattern of nucleotides. Tandem Repeats Finder is a program to locate and
display tandem repeats in DNA sequences. In order to use the program,
the user submits a sequence in FASTA format. There is no need to specify
the pattern, the size of the pattern or any other parameter. The
program's analysis is sent back to the user's web browser as two files,
a summary table file and an alignment file. The summary table contains
information about each repeat, including its location, size, number of
copies and nucleotide content. Clicking on the location indices for one
of the table entries opens a second web browser that shows an alignment
of the copies against a consensus pattern. The program is very fast,
analyzing sequences on the order of .5Mb in just a few
seconds. Submitted sequences may be up to 5Mb in length. Repeats with
pattern size in the range from 1 to 500 bases are detected. Sequence
information sent to the server is confidential and deleted after program
execution


---------------------------------------------------------------
 Anders Gorm Pedersen, cand.scient., Ph.D.  (gorm at cbs.dtu.dk)

 Center for Biological Sequence Analysis
 Technical University of Denmark
 Bldg 208, DK-2800 Lyngby, Denmark

 phone: (+45) 45 25 24 84
 fax:   (+45) 45 93 15 85

 Web: http://www.cbs.dtu.dk/gorm/
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